MICB425_portfolio

Module 01

Module 01 portfolio check

• Installation check
  • Completion status:
  • Comments:
• Portfolio repo setup
  • Completion status:
  • Comments:
• RMarkdown Pretty PDF Challenge
  • Completion status:
  • Comments:
• Evidence worksheet_01
  • Completion status:
  • Comments:
• Evidence worksheet_02
  • Completion status:
  • Comments:
• Evidence worksheet_03
  • Completion status:
  • Comments:
• Problem Set_01
  • Completion status:
  • Comments:
• Problem Set_02
  • Completion status:
  • Comments:
• Writing assessment_01
  • Completion status:
  • Comments:
• Additional Readings
  • Completion status:
  • Comments

Data science Friday

Installation check

Screenshot_GIT

Screenshot_GitHub

Screenshot_Rstudio

Portfolio repo setup

cd ~/documents
mkdir MICB425_portfolio
touch ID.txt
git init git add .
git commit -m“first commit”
git remote add origin https://remote_repository_URL
git remote -v
git push -u origin master

RMarkdown pretty PDF challenge

R Markdown PDF Challenge

The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.

http://phdcomics.com/ Comic posted 1-17-2018

Challenge Goals

The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)

hint: go to the PhD Comics website to see if you can find the image above
If you can’t find that exact image, just find a comparable image from the PhD Comics website and include it in your markdown

Here’s a header!

Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents)

Another header, now with maths

Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear! A calculator R is here:

1231521+12341556280987

## [1] 1.234156e+13

Table Time

Or maybe, after you’ve added those numbers, you feel like it’s about time for a table!
I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in the ^future.

library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")

I made this table with kable in the knitr package library

	speed	dist
	Min. : 4.0	Min. : 2.00
	1st Qu.:12.0	1st Qu.: 26.00
	Median :15.0	Median : 36.00
	Mean :15.4	Mean : 42.98
	3rd Qu.:19.0	3rd Qu.: 56.00
	Max. :25.0	Max. :120.00

And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh? Here’s ours! Include a fun gif of your choice!

Origins and Earth Systems

Evidence worksheet 01

Whitman et al 1998

Learning objectives

Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.

General questions

• What were the main questions being asked?

The main questions were:
- To determine the number of prokaryotes in different habitats
- Which habitats are the most important ones; contribute the most to the abundance of microbes
- The amount of carbon stored in prokaryotes
- Amounts of other nutrients (N, P) in prokaryotes
- Turnover rates of the microbes in different habitats
- Which habitats are the most productive ones
- Estimate prokaryotic diversity (higher turnover leads to more mutations, diversity)

• What were the primary methodological approaches used?

-Sampling of prokaryotes from different habitats, (top 200m of open ocean, ocean below 200m, different soils, subsurface in various dephts etc), quantification of cells in these samples.
-Estimation and extrapolation of cell abundances in habitats that could not be sampled.
-Research of data obtained from previous studies for estimations of cell abundance.
-Extrapolation, estimations, assumptions, mathematical formulas to calculate cell numbers, nutrient contents etc.
Examples of approaches:
-Open ocean: average cell density (cells/ml water), cell volume.-> estimate number of cells
-Subsurface: few samples taken, depth profile generated, extrapolation to 4km depth.
2nd approach: porosity of terrestrial surface 3%, 0.016% of pores occupied. -> use cell volume to calculate cell number
3rd: groundwater data for estimation
-Soil: estimations from direct cell counts from different soils

• Summarize the main results or findings.

There are three habitats that mainly contribute to earth’s prokaryotic abundance:
-Open ocean (1.2x 10²⁹ cells)
-Soil (2.6x 10²⁹ cells)
-Subsurfaces ( terrestrial, below 8m and marine below 10cm) (0.25-2.5x 10³⁰ cells)

Further important habitats but with minor contributions to total cell number:
- Animals, Leaves, Air

->Total number of prokaryotes estimated to 4-6x 10³⁰ cells

Total prokaryotic carbon: 350-550 Pg (1Pg= 10^15 g)
-> 60-100% of total carbon of plants

Total prokaryotic nutrients (N,P) are circa 10 fold more than in plants. (N: 85-130 Pg, P: 9-14 Pg)

Turnover times in different habitats:
- Ocean above 200m: 6-25 days
- Ocean below 200m: 300 days
- Soil: 2.5 years
- Subsurface: 1-2x 10³ years (likely inaccurate, too high number, indicates that current understanding of subsurface prokaryotes is incomplete)

Ocean above 200m has highest cellular productivity, highest number of cells per time produced. (8.2*10^29 cells/year)
-> highest cellular productivity leads to most mutation events, diversity

Total cellular production rate on earth: 1.7x 10³⁰ cells per year

-> Large population size and turnover rates generate a huge potential for microbial diversity.-> leads to the opportunity of emergence of new cycles, pathways
-> Number of prokaryotic species may be greatly underestimated

• Do new questions arise from the results?

The extremly long turnover rate for subsurface prokaryotes indicates that this habitat is not yet understood very well and needs to be further investigated

Determination of prokaryotic diversity:
- Huge prokaryotic populations with fast turnover rates (especially in open ocean) have the potential for a very large genetic diversity due to many mutation events. Prokaryotes have a much higher potential for simultaneous mutations than eukaryots and should therefore be differently treated in phylogenetic analyses. The number of prokaryotic species may be much higher than currently estimated through a DNA melting temperature method.
-> The diversity of prokaryotic species must be further investigated to understand the earths communities and its contribution to biogechemical processes.

-Paper is from 1980.-> How exact are the obtained numbers, estimations? Are there better technologies, more samples available to repeat calculations (especially for subsurface samples)?
-Has abundance and diversity of microbes changed since 1980?

• Were there any specific challenges or advantages in understanding the paper (e.g. did the authors provide sufficient background information to understand experimental logic, were methods explained adequately, were any specific assumptions made, were conclusions justified based on the evidence, were the figures or tables useful and easy to understand)?

The assumptions and methods of the calculations were often not very well explained or completely absent. As most of the results in this paper are based on assumptions and estimations, it would have been useful if they were more transparent in their calculations. Therefore, also some more detailed discussion about the precision of the obtained numbers with error estimates or confidence intervals for example would have been usefull.

Problem set 01

Learning objectives:

Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.

Specific questions:

• What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.

Open ocean: Total 1.2x 10²⁹ cells
-Top 200m: 3.6x 10²⁸
-Below 200m (incl. 10 cm of sediment): 8.2x 10²⁸

Soil: 2.6x 10²⁹ cells

Subsurfaces: ~3.8x 10³⁰ cells (uncertain, estimation)

• What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?

Upper 200m: 3.6x 10²⁸ cells
->2.9x 10²⁷ autotrophs (cyanobacteria)
8.06% are autotrophs (cyanobacteria)

These 8% of autotrophic bacteria have to assimilate enough carbon to sustain the requirement of additional carbon from the 92% heterotrhopic cells.

This ratio means that 8% of assimilating autotrophs can sustain the need of additional carbon from outside the oceanic carbon cycle for the 92% of heterotrophes. Therefore, there is much more carbon cycling within the ocean than new carbon is fixed from the atmosphere to the ocean or that carbon is ‘lost’ from the ocean to the atmosphere.

• What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?

Autotroph: CO2 as carbon source used. Fix inorganic carbon to biomass.
Heterotroph: not CO2 as carbon source.-> organic carbon needed.
Lithotroph: inorganic electron donor like NH3, H2S

• Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?

4km below the surface. (4 km below terrestrial surface or marine sediments)
At 4km below surface, the temperature is about 125 degrees celsius, which is the temperature-limit for prokaryotes to live. In terrestrial habitat, temperature rises about 22 degrees celsius per km.

• Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?

Up to 77km (But not really living cells up there, only transient state, spores…)
More realistic: 20km
Limiting factor: cold temperature (up to -90 degrees), radiation, low pressure, no nutrients
-> Mnt. Everest: 8.8km + 20km on top-> 28.8 km

• Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?

Mariana trench: ~10.9 km deep, from this point, microbes can live up to 4km further down below marine sediment-surface.
-> from 20km on top of Mnt. Everest to 4km below Mariana trench -> total of 44 km

• How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)

For annual cellular production, population size and growth rate must be taken into account.

-> Population size x Turnover rate (years)= Annual cellular production
->Ocean above 200m:
Pop size = 3.6x 10²⁸ cells
Turnover time in days: 16 -> Turnover rate = 365/16= 22.81 per year
-> 3.6x 10²⁸ Cells x 22.81 Turnovers per year = 8.2x 10²⁹ cells per year

->in soil:
pop. size= 2.6x 10²⁹ cells
Turnover rate = 0.4 per year (= 365/900)
-> 2.6x 10²⁹ x 0.4= 10²⁹ cells per year

• What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?

Net productivity in ocean: 51 Pg/year
Prokaryotic carbon in ocean: 0.7-2.9 Pg
Carbon in one cell: 10 fg/Cell -> 20 x 10^-30 pg/cell
3.6*10²⁸ cells x 20x 10^-30 pg/cell= 0.72 Pg of carbon in marine heterotrophes
Carbon efficiency: 20%. But factor used in paper: 4 (!?)
4 x 0.72 Pg = 2.88 Pg/year
85% of net productivity consumed in upper 200m.-> 51Pg x 0.85= 43.35 Pg
43 pg/yr / 2.88 pg/yr = 14.9 Turnovers per year -> Turnover every 24.5 days.

85% of net productivity consumed in upper 200m.-> 51Pg x 0.85= 43.35 Pg

43.35 Pg / 0.7 Pg = 61 per year turnover rate max
43.35 Pg / 2.9 = 15 per year turnover rate min

-> the net productivity has to be four times (not 5?!) the amount of the carbon of prokariots to support their turnover.
- turnover rate can not exceed 15-60 per year.
Relationship varies because different fractions of the primary productivity reach different depths in different habitats. ( in soil, carbon gets burried much slower than carbon can sink in the ocean.- in ocean more carbon available when closer to the surface because more sunlight->more autotrophs present, more photosynthesis possible.

• How were the frequency numbers for four simultaneous mutations in shared genes determined for marine heterotrophs and marine autotrophs given an average mutation rate of 4 x 10^-7 per DNA replication? (Provide an example of the calculation with units. Hint: cell and generation cancel out)

(4 x 10^-7 mutations per gene per generation)⁴ = 2.56 x 10^-26 mutation rate for 4 simoultanous mutations per gene per generation
3.6 x 10²⁸cells x 22.8 turnovers per year = 8.2 x 10²⁹ cells per year
8.2 x 10²⁹cells per year x 2.56 x 10^-26 mutations per generation = 2.1 x 10⁴ times per year => four simoultanous mutations every 0.4 hours.

• Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?

Genetic diversity and adaptive potential might be much higher than previously expected. The number of prokaryotic species might be much higher than estimatad with DNA melting temperature method. The high diversity leads to the potential to adapt to changing environments and new metabolic pathways and cycles can emerge. Through the large number of prokaryotic cells and their high diversity, the microbes even have the potential to alter global nutrient cycles.

Microbes can not only diversify by point mutations, but also by bigger rearrangements in the genome (inversion, duplication, deletion etc). Else, genes (plasmids) could be transferred during conjugation, transformation or transduction, which allows fast adaptation through horizontal gene-transfer.

• What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?

The enormous abundance of prokaryotes and the high turnover rates lead to a huge diversity. New mutations leading to new metabolic functions, pathways and cycles occur continously. Therefore, the metabolic potential is not only unimaginably high, but can also expand constantly to previously unknown emerging properties. Thus, microbes have the potential to significantly participate in and alter important biogeochemical cycles.

Module 01 references

Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95(12):6578–6583. PMC33863

Evidence worksheet 02

Key events in the evolution of Earth systems

Hadean: 4.6 Ga: Formation of earth
4.5 Ga: Moon formed by impact of inner planet. Induced spin, tilt of Earth, leading to day/ night cyles and seasons.
4.4 Ga: Oldest zircoins, formation of Oceans, atmosphere 4.3-3.8 Ga: Heavy bombardment of Earth 4.1 Ga: First evidence for life: Carbon isotopes preserved
4.0 Ga: Plate subduction
- Oldest rock: acasta gneiss in Canada. -> Silica-rich rocks - water Oceans needed to provide cool, hydrated lithospheric plates to create rocks
- CO2 as greenhouse gas, CO2 rich ocean.-> reacts with basalt to form carbonates.-> CO2 decreases, atmosphere cools down-> surface temperature glacial -methane as greenhouse gas

Archaean: 3.8 Ga: Oldest sedimentary rocks,
Carbon isotopes: Evidence for life in sedimentary rocks in greenland Photosynthesis possible, Rubisco -Cyanobacteria 3.5 Ga: Evidence for photosynthesis in microfossils, stromatolites, fossil biofilms -rubisco -Sun weak, methane as greenhouse gas, warming shield
3 Ga: Glaciation because of oxygen production, less methanogen production.- less greenhouse effect
-Life on land: great oxydation event-> glaciation
-Large carbon isotope signals for carbon fixation -well developed stromatolites in ontario, south africa

2.7 Ga: -well developed stromatolites -direct evidence for life: molecular fossils of biological lipids from western australia. -hydrocarbon biomarkers characteristic of cyanobacteria imply oxygenic photosynthesis -Steranes as evidence for presence of eukaryotes

2.2 Ga: -Complex eukaryotes, oxygen level increased sharply -Change of anaerobic (microaerobic) air to oxic air leads to significant change of living biota.-> anaerobes go extinct.
-Cellular cybernetic switch between mitochondria, chloroplasts. - may control link between photosynthesis and N fixation.

Proterozoic:
-1.8 Ga: Eukaryotes, algae, symbiosis. - changing carbon cycle, several global glaciations.- snowball Earth -macroscopic life forms

-540 Ma: End of precambrian: cambrian explosion- emergence, diversification of animals. -expansion of mulitcellular evolution

phanerozoic: 400 Ma: devonian explosion: land plants, gigantism -strong increased oxygenation of atmosphere -Carboniferous period: fish, cephalopods, corals

300 Ma: Permian extinction (95% of species) -followed by rapid speciation, rise of dinosaurs -Formation of pangea, dry, harsh climate

-66 Ma: Cretaceous-tertiary extinction event - dramatic global warming -diversification of mammals, increasing size of mammals -dominating forest

23 Ma: neogene; Ice age

6 Ma: First hominins

2.6 Ma: Quaternary period

200’000 BP: Homo sapiens appears

Dominant physical/ chemical characteristics of Earth systems

4.6 Ga:
-High CO2 pressure; heat radiated to space -500 degrees Celsius
-CO2 tied up in carbonate minerals (limestone) -Ocean filled with water -Water as greenhouse gas, as vapour high in atmosphere, phtolysed into hydrogen and oxygen, hydrogen lost to space

4.5 - 4 Ga: -100 degrees Celsius
-Many meteorite impacts, heating up earth to >100 degrees. -> ocean vapourized -Seawater chemistry controlled by volcanism -Ice house, CO2 rising as greenhouse gas

3.8 Ga: -Meteorite bombardment halted.-> seawater chemistry stabilized -sulphur reduction -methanogenesis: greenhouse gas, heating up earth (Earth would have been glacial without methane shield because of weaker sun)

3.5 Ga: -Earth still anoxic -Hydrothermal, volcanogenic habitats -Microbes spread on coastal fringes, deeper water, deep hydrothermal vents

2.7 Ga: -well developed stromatolites

2.2 Ga: -oxygen level sharply increased.-> complex eukaryotes -Rocks recognized as red beds-> indicate oxidation -Change of anaerobic (microaerobic) air to oxic air leads to significant change of living biota.-> anaerobes go extinct.

Module 1 assay

“Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides.”

Ever since the emergence of humans, we have been interacting with microbes. We live in symbiosis with microbes in many different aspects, which rises the important question whether we could survive without them. Microbial life emerged about 4.1 billion years before the first humans developed, which proofs that microbes can easily live without us. In contrast, confirming that humans cannot survive without the global catalysis provided by microbes, is much more challenging. Several aspects need to be considered in order to answer the question whether humans rely on the presence of microbes. Firstly, after their emergence, the microbes rapidly spread all over the earth and rose to incredible numbers of individuals. Secondly, fast reproduction and constant turnover of the cells leads to massive requirements of nutrients and thereby promotes the global turnover of these nutrients. The fast reproduction of microbes further generates an enormous genetic diversity through mutations, which allows the microbes to constantly adapt present pathways or even generate new metabolic processes. Through this extremely high abundance and diversity, microbes developed a massive potential not only to actively participate in, but also to significantly alter important biogeochemical cycles, which can be shown by several examples covered in this assay. Lastly, this potential for global catalysis leads to important, microbially driven environmental transformations on Earth, creating an inhabitable atmosphere. This not only allowed for the emergence of more complex organisms and the human species, but will also be important for human survival in the future.

Microbes have a massive potential to impact global cycles because of their sheer number of cells present. They account for by far the biggest part of the number of organisms alive on earth and arguably also the greatest part of nutrients stored in living beings. The number of prokaryotes living on earth could be obtained by cell counts of probes sampled from several different habitats. Subsequent projection and extrapolation for habitats not available for sampling led to an estimation of 4-6*1030 cells present (Whitman, Coleman, and Wiebe 1998). Considering average values of nutrient contents per cell, leads to the conclusion that microbes totally contain 60-100% of the amount of carbon stored in plants. The fraction of nitrogen and phosphorus stored in microbes is even higher, with about ten times more of these elements stored in microbes than in plants. These numbers show, that through their enormous abundance and capacity, microbes technically have the potential to provide important global catalysis.

In addition to the huge number of microbial cells, their fast turnover rates generate an even higher potential of the microbes to significantly catalyze and transform global cycles. An average turnover rate of 22 turnovers per year leads to about 8.2*1029 heterotrophic cells produced every year, just in the upper 200 meters of the ocean. Therefore, the vast amounts of cells continuously being produced further explains their impact on global cycles as their constant metabolism leads to massive requirements and turnover of nutrients. The constant turnover of prokaryotes additionally offers the opportunity to generate an enormous genetic diversity through billions of mutation events. The large genetic variation leading to continuous adaptation through evolution enables the bacteria to constantly generate new metabolic pathways and cycles. In summary, the fast microbial reproduction accounts for high nutrient requirement, global circulation of these nutrients and generation of metabolic diversity through evolving cells. This allows for the conclusion, that microbes have the potential to significantly transform the environment and even catalyze global cycles in such a powerful way that humans become dependent on their presence on Earth.

The enormous abundance, turnover and diversity provides a huge potential for the microbes to actively contribute to the composition of Earth’s properties. These contributions thereby are of such importance that humans would not be able to survive without microbes providing them, which can be shown by several examples. Firstly, marine microorganisms are responsible for the generation of nearly all of the oxygen present in the atmosphere (Kasting and Siefert 2002). The oxygen produced by plants only contributes to a small fraction of atmospheric oxygen because most of the O2 produced by plants is used up again by their own respiratory processes and upon decay of dead plant material. Therefore, the oxygen produced by microbes is substantial for human respiration and hence, also existence. Second, Earth’s redox state depends mostly on microbial life and therefore is an emergent property of their existence (Falkowski, Fenchel, and Delong 2008). This means, the global fluxes of some of the most important elements (H, C, N, O, S) are controlled in large parts by redox reactions which are catalyzed by prokaryotes. Thus, microbial photosynthesis not only provides humans with breathable air, but also drives the Earth’s oxidation in general, and finally, supplies heterotrophic organisms with reduced carbon. Further, not only photosynthesis, but many other microbial processes contribute to important global nutrient cycles. One example for a cycle largely controlled by microbes is the nitrogen cycle. Microbes catalyze all the steps present in the global nitrogen cycle and thereby control the oxidation state in which the nitrogen species are present in Earth’s atmosphere, soil and oceans. Many other prokaryotes and eukaryotes, that cannot process atmospheric nitrogen, rely on the supply of these nitrogen species provided by nitrogen-fixing microbes. Also humans rely on fixed nitrogen, which initially is provided by microbes and wanders through the food chain until eventually taken up as part of the human nourishment. All of these examples show, that the global nutrient cycles which are in large parts controlled by microbes, are of such importance, that human existence relies on their catalysis provided by microbes.

The potential of microbes to catalyze global processes does not only affect nutrient cycles, but also the global environment and climate. Microorganisms can significantly change the climate by altering the atmospheric composition. The production of several gases like methane and nitrous oxide strongly influences the global climate through the greenhouse effect. The great importance of this effect for the survival of organisms can be shown not only for present days, but also for early stages in time. In the distant past, about 3.5 billion of years ago, microbial methane production might have contributed to a global shield, warming up the planet (Nisbet and Sleep 2001). At this time, the sun was much weaker than today and therefore, without a greenhouse gas like methane, Earth would have been completely frozen over. By keeping the earth from freezing, this methane shield might have allowed for fast reproduction, leading to evolution and the emergence of more complex life-forms. About 500 million years later, microbes again significantly transformed the environment. The emergence of photosynthetic cyanobacteria led to a strong increase of the oxygen level in the atmosphere. This resulted in decreased viability of methanogenic organisms and therefore decreased methane concentrations, which in turn reduced the greenhouse effect. The consequence was a global glaciation, again significantly changing the composition of organisms capable of living on Earth. In summary, in the absence of microbes, the global environment with its properties as present now, could not have been created. In a world depleted of the global catalysis provided by microbes, Earth’s environment would have been very unfavorable for the emergence of complex life forms as they are present today. As the past times show, a stable environment, which can be provided and maintained by microbes, will also be necessary for humans to live in future times. If humans wanted to survive without microbes, they would have to artificially control all the cycles currently run by microbes. This, however, is most likely not possible. Humans will not be able to replace all the microbially driven cycles in an efficient way. We are not able to generate machines catalyzing processes as efficient as microbes do after millions of years of evolution. Further, as microbial diversity is unimaginably high, the range of the processes they catalyze can always adapt quickly to changing conditions. Humans will not be able to adapt their engineered machines fast enough in order to provide sufficient flexibility to changing demands.

In summary, the enormous number of prokaryotic cells present, their fast turnover and the high genetic diversity offer an unimaginable potential for the microbes to significantly contribute to the presence and properties of biogeochemical cycles. Microbes provide a global environment-composition which allowed for the emergence of humans and will also in the future be necessary for our persistence. From the beginning of our existence, we have been living in symbiosis with microbes. We do not only interact with microbes living in and on our bodies, but also with the global biogeochemical cycles they are a significant part of. Artificially replacing all of the processes provided by microbes will not be possible in a sufficient way. Therefore, existence of human life without the presence of microbes is most likely not possible as our survival strongly depends on stable global cycles, kept intact by microbes. Microbes have been the guardians of global metabolism for billions of years(Waters et al. 2016). It is very unlikely that humans could further exist without microbes present, continuously guarding global metabolic processes. A new question that arises is however, how likely it is, that the human race eventually manages to destroy this essential function of the microbes as guardians of global metabolism.

References

Falkowski, P. G., T. Fenchel, and E. F. Delong. 2008. ‘The microbial engines that drive Earth’s biogeochemical cycles’, Science, 320: 1034-9. Kasting, J. F., and J. L. Siefert. 2002. ‘Life and the evolution of Earth’s atmosphere’, Science, 296: 1066-8. Nisbet, E. G., and N. H. Sleep. 2001. ‘The habitat and nature of early life’, Nature, 409: 1083. Waters, Colin N., Jan Zalasiewicz, Colin Summerhayes, Anthony D. Barnosky, Clément Poirier, Agnieszka Gałuszka, Alejandro Cearreta, Matt Edgeworth, Erle C. Ellis, Michael Ellis, Catherine Jeandel, Reinhold Leinfelder, J. R. McNeill, Daniel deB. Richter, Will Steffen, James Syvitski, Davor Vidas, Michael Wagreich, Mark Williams, An Zhisheng, Jacques Grinevald, Eric Odada, Naomi Oreskes, and Alexander P. Wolfe. 2016. ‘The Anthropocene is functionally and stratigraphically distinct from the Holocene’, Science, 351. Whitman, W. B., D. C. Coleman, and W. J. Wiebe. 1998. ‘Prokaryotes: the unseen majority’, Proc Natl Acad Sci U S A, 95: 6578-83.